Using historical dip net data to infer absence of flatwoods salamanders in stochastic environments

Local extinction and undetected presence are two very different biological phenomena, but they can be challenging to differentiate. Stochastic environments hamper the development of standardized monitoring schemes for wildlife, and make it more challenging to plan and evaluate the success of conservation efforts. To avoid reintroductions of species at risk that could jeopardize extant populations, managers attempting translocation events require a higher level of confidence that a failure to confirm presence represents a true absence. For many pond breeding amphibians, monitoring of the breeding population occurs indirectly through larval surveys. Larval development and successful recruitment only occurs after a sequence of appropriate environmental conditions, thus it is possible for a breeding population of adults to exist at a site but for detectability of the species to be functionally zero. We investigate how annual variability in detection influences long-term monitoring efforts of Reticulated Flatwoods Salamanders (Ambystoma bishopi) breeding in 29 wetlands in Florida. Using 8 years of historic dip net data, we simulate plausible monitoring scenarios that incorporate environmental stochasticity into estimates of detection probability. We found that annual variation in environmental conditions precluded a high degree of certainty in predicting site status for low-intensity monitoring schemes. Uncertainty was partly alleviated by increasing survey effort, but even at the highest level of sampling intensity assessed, multiple years of monitoring are required to confidently determine presence/absence at a site. Combined with assessments of habitat quality and landscape connectivity, our results can be used to identify sites suitable for reintroduction efforts. Our methodologies can be generally applied to increase the effectiveness of surveys for diverse organisms for which annual variability in detectability is known.

Feral swine Sus scrofa: a new threat to the remaining breeding wetlands of the Vulnerable reticulated flatwoods salamander Ambystoma bishopi

Feral swine Sus scrofa have been implicated as a major threat to sensitive habitats and ecosystems as well as threatened wildlife. Nevertheless, direct and indirect impacts on threatened species (especially small, fossorial species) are not well documented. The decline of the U.S. federally endangered reticulated flatwoods salamander Ambystoma bishopi, categorized as Vulnerable on the IUCN Red List, has been rapid and there are few remaining breeding locations for this species. The flatwoods salamander depends on complex herbaceous vegetation in all life stages, including eggs, larvae and adults. Historically sets of hog tracks have been observed only occasionally in the vicinity of monitored reticulated flatwoods salamander breeding wetlands, and damage to the wetlands had never been recorded. However, during the autumn–winter breeding season of 2013–2014 we observed a large increase in hog sign, including extensive rooting damage, in known flatwoods salamander breeding wetlands. Our objective was to assess the amount of hog sign and damage in these wetlands and to take corrective management actions to curb additional impacts. Of 28 wetlands surveyed for hog sign, presence was recorded at 68%, and damage at 54%. Of the 11 sites known to be occupied by flatwoods salamanders in 2013–2014, 64% had presence, and 55% had damage. We found that regular monitoring of disturbance in wetland habitats was a valuable tool to determine when intervention was needed and to assess the effectiveness of intervention. Habitat damage caused by feral hogs poses a potentially serious threat to the salamanders, which needs to be mitigated using methods to control and exclude hogs from this sensitive habitat.

Assessment of Environmental DNA for Detecting Presence of Imperiled Aquatic Amphibian Species in Isolated Wetlands

Environmental DNA (eDNA) is an emerging tool that allows low-impact sampling for aquatic species by isolating DNA from water samples and screening for DNA sequences specific to species of interest. However, researchers have not tested this method in naturally acidic wetlands that provide breeding habitat for a number of imperiled species, including the frosted salamander (Ambystoma cingulatum), reticulated flatwoods salamanders (Ambystoma bishopi), striped newt (Notophthalmus perstriatus), and gopher frog (Lithobates capito). Our objectives for this study were to develop and optimize eDNA survey protocols and assays to complement and enhance capture-based survey methods for these amphibian species. We collected three or more water samples, dipnetted or trapped larval and adult amphibians, and conducted visual encounter surveys for egg masses for target species at 40 sites on 12 different longleaf pine (Pinus palustris) tracts. We used quantitative PCRs to screen eDNA from each site for target species presence. We detected flatwoods salamanders at three sites with eDNA but did not detect them during physical surveys. Based on the sample location we assumed these eDNA detections to indicate the presence of frosted flatwoods salamanders. We did not detect reticulated flatwoods salamanders. We detected striped newts with physical and eDNA surveys at two wetlands. We detected gopher frogs at 12 sites total, three with eDNA alone, two with physical surveys alone, and seven with physical and eDNA surveys. We detected our target species with eDNA at 9 of 11 sites where they were present as indicated from traditional surveys and at six sites where they were not detected with traditional surveys. It was, however, critical to use at least three water samples per site for eDNA. Our results demonstrate eDNA surveys can be a useful complement to traditional survey methods for detecting imperiled pond-breeding amphibians. Environmental DNA may be particularly useful in situations where detection probability using traditional survey methods is low or access by trained personnel is limited.